http://askubuntu.com/questions/6176/how-do-i-upgrade-from-x86-to-x64-without-losing-settings

1) Backup your /etc and /home folders (I have /home as its own partition, you may need more folders if you have any custom folders… or /var/www if you have Apache, maybe backup databases if you had any). You may use for example fsarchiver.

2) Run dpkg --get-selections > installed-software to save the list of installed software, change content of exported package list, replace word “deinstall” to “installed“, backup the file “installed-software“.

3) Install the x64 version over existing system without formating volume, create the same users. Restore the /etc and /home folders and the “installed-software” file.

4) Run dpkg --set-selections < installed-software, then run apt-get dselect-upgrade to install the previously installed software.